0.1 Publicly available data from JHU Biobank

We used the publicly available JHU Biobank RNASeq data stored in project : syn20812185 for this analysis.

We then used TMM normalization to prepare the dataset for differential gene expression analysis.

 

0.2 Differential gene expression analysis in samples:

We used limma-edgeR based analysis to find differentially expressed genes in the TMM normalized dataset.

A point to note:

  • All MPNST samples except one are males while all PNF samples except one are femmales. So there may be a sex related effect on the analysis that we dont have a good way to mitigate.
  • The number of MPNST samples are extremely limited (n=4), so these results should be evaluated with more samples when possible

The plot below shows genes that are significantly overexpressed in MPNST compared to PNF or NF (logFC > 4) in red. The dots in blue refer to genes that are significantly underexpressed in MPNST compared to PNF or NF (logFC < -4). The thresholds of fold change have been arbitrarily chosen for ease of visualization in the volcano plot shown below.

0.2.1 MPNST vs PNF

 

0.2.1.1 DEG Analysis

Differential expression of genes in MPNST and pNF tumor types. Above shows a volcano plot highlighting significantly upregulated genes in red and downregulated genes in blue

Differential expression of genes in MPNST and pNF tumor types. Above shows a volcano plot highlighting significantly upregulated genes in red and downregulated genes in blue

Differential expression of genes in MPNST and pNF tumor types. Above shows a volcano plot highlighting significantly upregulated genes in red and downregulated genes in blue

Differential expression of genes in MPNST and pNF tumor types. Above shows a volcano plot highlighting significantly upregulated genes in red and downregulated genes in blue

Differential expression of genes in MPNST and pNF tumor types. Above shows a volcano plot highlighting significantly upregulated genes in red and downregulated genes in blue

Differential expression of genes in MPNST and pNF tumor types. Above shows a volcano plot highlighting significantly upregulated genes in red and downregulated genes in blue

 

0.2.1.2 Pathway analysis

## [1] "Enrichment Plot of Cluster 1 genes"

## [1] "Enrichment Plot of Cluster 2 genes"

## [1] "Enrichment Plot of Cluster 3 genes"

## [1] "List of genes in Cluster 3"
##  [1] "AMPH"      "ARHGAP11A" "BIRC5"     "BYSL"      "CACNA1A"   "CCNA2"    
##  [7] "CCNB1"     "CCNF"      "CDC20"     "CDCA5"     "CILP2"     "COL13A1"  
## [13] "CYTL1"     "ELFN1"     "EPOP"      "FAM155A"   "FANCI"     "GALNT14"  
## [19] "HAPLN3"    "IGF2BP3"   "KRT18"     "NCAPG"     "NCAPH"     "NUSAP1"   
## [25] "OSBPL6"    "PLK1"      "PMAIP1"    "PRC1"      "PTTG1"     "RAB42"    
## [31] "RRM2"      "SEC61G"    "SERINC2"   "SIX4"      "SLC16A3"   "SLC39A11" 
## [37] "SPAG5"     "TNFSF9"    "TPX2"      "TSTA3"     "ULBP1"

 

0.2.2 MPNST vs NF

0.2.2.1 DEG Analysis

Differential expression of genes in MPNST and NF tumor types. Above shows a volcano plot highlighting significantly upregulated genes in red and downregulated genes in blue

Differential expression of genes in MPNST and NF tumor types. Above shows a volcano plot highlighting significantly upregulated genes in red and downregulated genes in blue

Differential expression of genes in MPNST and NF tumor types. Above shows a volcano plot highlighting significantly upregulated genes in red and downregulated genes in blue

Differential expression of genes in MPNST and NF tumor types. Above shows a volcano plot highlighting significantly upregulated genes in red and downregulated genes in blue

Differential expression of genes in MPNST and NF tumor types. Above shows a volcano plot highlighting significantly upregulated genes in red and downregulated genes in blue

Differential expression of genes in MPNST and NF tumor types. Above shows a volcano plot highlighting significantly upregulated genes in red and downregulated genes in blue

 

0.2.2.2 Pathway analysis

## [1] "Enrichment Plot of Cluster 1 genes"

## [1] "Enrichment Plot of Cluster 2 genes"

## [1] "List of genes in Cluster 2 (cluster with PLK1)"
##  [1] "ACAN"     "ADAMTS17" "APBA2"    "BIRC5"    "CACNA1A"  "CBX2"    
##  [7] "CCNA2"    "CCNF"     "CDC20"    "CDCA5"    "CILP2"    "COL13A1" 
## [13] "DPYSL4"   "ELFN1"    "EPOP"     "GALNT14"  "HOXA5"    "IGF2BP3" 
## [19] "IL4I1"    "JPH4"     "KIF15"    "KIFC1"    "KRT8"     "LRRN2"   
## [25] "MSX2"     "NCAPG"    "NRK"      "PLK1"     "RAB42"    "SAMD14"  
## [31] "SERINC2"  "SHISA2"   "SIX1"     "SIX4"     "SNCAIP"   "SPEG"    
## [37] "SUGCT"    "TK1"      "TNFSF9"   "TRIM59"   "ULBP1"    "VPS37D"
## [1] "Enrichment Plot of Cluster 3 genes"

## [1] "Enrichment Plot of Cluster 4 genes"